From a humorous post to a detailed quantum-chemical study: isocyanate synthesis revisited

Isocyanates play an essential role in modern manufacturing processes, especially in polyurethane production. There are numerous synthesis strategies for isocyanates both under industrial and laboratory conditions, which do not prevent searching for alternative highly efficient synthetic protocols. Here, we report a detailed theoretical investigation of the mechanism of sulfur dioxide-catalyzed rearrangement of phenylnitrile oxide into phenyl isocyanate, which was first reported in 1977. The DLPNO-CCSD(T) method and up-to-date DFT protocols were used to perform a highly accurate quantum-chemical study of the rearrangement mechanism. An overview of various organic and inorganic catalysts has revealed other potential catalysts, such as sulfur trioxide and selenium dioxide. Furthermore, the present study elucidated how substituents in phenylnitrile oxide influence reaction kinetics. This study was performed by a self-organized collaboration of scientists initiated by a humorous post on the VK social network.

Regularized weighted sine least-squares spectral analysis for gas electron diffraction data

Here, we present a new approach for obtaining radial distribution functions (RDF) from the electron diffraction data using a regularized weighted sine least-squares spectral analysis. It allows for explicitly transferring the measured experimental uncertainties in the reduced molecular scattering function to the produced RDF. We provide a numerical demonstration, discuss the uncertainties and correlations in the RDFs, and suggest a regularization parameter choice criterion. The approach is also applicable for other diffraction data, e.g., for x-ray or neutron diffraction of liquid samples.

Describing nuclear quantum effects in vibrational properties using molecular dynamics with Wigner sampling

In this work we discuss the generally applicable Wigner sampling and introduce a new, simplified Wigner sampling method, for computationally effective modeling of molecular properties containing nuclear quantum effects and vibrational anharmonicity. For various molecular systems test calculations of (a) vibrationally averaged rotational constants, (b) vibrational IR spectra and (c) photoelectron spectra have been performed. The performance of Wigner sampling has been assessed by comparing with experimental data and with results of other theoretical models, including harmonic and VPT2 approximations. The developed simplified Wigner sampling method shows advantages in application to large and flexible molecules.

Metadynamics simulations with Bohmian-style bias potential

Here, we present a parametrization of the metadynamics simulations for reactions involving breaking the chemical bonds along a single collective variable coordinate. The parameterization is based on the similarity between the bias potential in metadynamics and the quantum potential in the de Broglie-Bohm formalism. We derive the method and test it on two prototypical reaction types: proton transfer and breaking of the cyclohexene cycle (reversed Diels-Alder reaction).

Pump-probe spectroscopy of chiral vibrational dynamics

A planar molecule may become chiral upon excitation of an out-of-plane vibration, changing its handedness during half a vibrational period. When exciting such a vibration in an ensemble of randomly oriented molecules with an infrared laser, half of the molecules will undergo the vibration phase-shifted by π compared to the other half, and no net chiral signal is observed. This symmetry can be broken by exciting the vibrational motion with a Raman transition in the presence of a static electric field. Subsequent ionization of the vibrating molecules by an extreme ultraviolet pulse probes the time-dependent net handedness via the photoelectron circular dichroism. Our proposal for pump-probe spectroscopy of molecular chirality, based on quantum-chemical theory and discussed for the example of the carbonyl chlorofluoride molecule, is feasible with current experimental technology.

The kinetic energy of PAH dication and trication dissociation determined by recoil-frame covariance map imaging

We investigated the dissociation of dications and trications of three polycyclic aromatic hydrocarbons (PAHs), fluorene, phenanthrene, and pyrene. PAHs are a family of molecules ubiquitous in space and involved in much of the chemistry of the interstellar medium. In our experiments, ions are formed by interaction with 30.3 nm extreme ultraviolet (XUV) photons, and their velocity map images are recorded using a PImMS2 multi-mass imaging sensor. Application of recoil-frame covariance analysis allows the total kinetic energy release (TKER) associated with multiple fragmentation channels to be determined to high precision, ranging 1.94-2.60 eV and 2.95-5.29 eV for the dications and trications, respectively. Experimental measurements are supported by Born-Oppenheimer molecular dynamics (BOMD) simulations.

Structures of the (Imidazole)nH+ ... Ar (n=1,2,3) complexes determined from IR spectroscopy and quantum chemical calculations

Here, we present new cryogenic infrared spectra of the (Imidazole)$$_{n}\mathrm{H}^{+}$$ n H + (n=1,2,3) ions. The data was obtained using helium tagging infrared predissociation spectroscopy. The new results were compared with the data obtained by Gerardi et al. (Chem. Phys. Lett. 501:172–178, 2011) using the same technique but with argon as a tag. Comparison of the two experiments, assisted by theoretical calculations, allowed us to evaluate the preferable attachment positions of argon to the (Imidazole)$$_{n}\mathrm{H}^{+}$$ n H + frame. Argon attaches to nitrogen-bonded hydrogen in the case of the (Imidazole)H$$^+$$ + ion, while in (Imidazole)$$_{2}\mathrm{H}^{+}$$ 2 H + and (Imidazole)$$_{3}\mathrm{H}^{+}$$ 3 H + the preferred docking sites for the argon are in the center of the complex. This conclusion is supported by analyzing the spectral features attributed to the N–H stretching vibrations. Symmetry adapted perturbation theory (SAPT) analysis of the non-covalent forces between argon and the (Imidazole)$$_{n}\mathrm{H}^{+}$$ n H + (n=1,2,3) frame revealed that this switch of docking preference with increasing complex size is caused by an interplay between induction and dispersion interactions.

Double Proton Transfer Across a Table: The Formic Acid Dimer-Fluorobenzene Complex

Proton transfer via tunneling is a fundamental quantum‐mechanical phenomenon. We report rotational spectroscopy measurements of this process in the complex of the formic acid dimer with fluorobenzene. The assignment of the spectrum indicates that this complex exists in the form of a π–π stacked structure. Each rotational transition of the parent isotopologue exhibits splitting. Isotopic substitution experiments show that the spectral splitting results from double‐proton transfer tunneling in the formic acid dimer. Presence of fluorobenzene as a neighboring molecule does not quench the double proton transfer in the formic acid dimer but decreases its tunneling splitting from 341(3) MHz to 267.608(1) MHz. Calculations suggest that the presence of the weakly bounded fluorobenzene does not influence the activation energy of the proton transfer. The fluorobenzene is reoriented with respect to the formic acid dimer during the course of the reaction, slowing down the proton transfer motion.

A simplistic computational procedure for tunneling splittings caused by proton transfer

In this manuscript, we present an approach for computing tunneling splittings for large amplitude motions. The core of the approach is a solution of an effective one-dimensional Schrödinger equation with an effective mass and an effective potential energy surface composed of electronic and harmonic zero-point vibrational energies of small amplitude motions in the molecule. The method has been shown to work in cases of three model motions: nitrogen inversion in ammonia, single proton transfer in malonaldehyde, and double proton transfer in the formic acid dimer. In the current work, we also investigate the performance of different DFT and post-Hartree–Fock methods for prediction of the proton transfer tunneling splittings, quality of the effective Schrödinger equation parameters upon the isotopic substitution, and possibility of a complete basis set (CBS) extrapolation for the resulting tunneling splittings.

Switching Hydrogen Bonding to π-Stacking: The Thiophenol Dimer and Trimer

We used jet-cooled broadband rotational spectroscopy to explore the balance between π-stacking and hydrogen-bonding interactions in the self-aggregation of thiophenol. Two different isomers were detected for the thiophenol dimer, revealing dispersion-controlled π-stacked structures anchored by a long S-H···S sulfur hydrogen bond. The weak intermolecular forces allow for noticeable internal dynamics in the dimers, as tunneling splittings are observed for the global minimum. The large-amplitude motion is ascribed to a concerted inversion motion between the two rings, exchanging the roles of the proton donor and acceptor in the thiol groups. The determined torsional barrier of B₂ = 250.3 cm^-1 is consistent with theoretical predictions (290-502 cm^-1) and the monomer barrier of 277.1(3) cm^-1. For the thiophenol trimer, a symmetric top structure was assigned in the spectrum. The results highlight the relevance of substituent effects to modulate π-stacking geometries and the role of the sulfur-centered hydrogen bonds.

Approaching black-box calculations of pump-probe fragmentation dynamics of polyatomic molecules

A general framework for the simulation of ultrafast pump-probe time resolved experiments based on Born-Oppenheimer molecular dynamics (BOMD) is presented. Interaction of the molecular species with a laser is treated by a simple maximum entropy distribution of the excited state occupancies. The latter decay of the electronic excitation into the vibrations is based on an on-the-fly estimation of the rate of the internal conversion, while the energy is distributed in a thermostat-like fashion. The approach was tested by reproducing the results of previous femtosecond studies on ethylene, naphthalene and new results for phenanthrene.

Application of classical simulations for the computation of vibrational properties of free molecules

In this study, we investigate the ability of classical molecular dynamics (MD) and Monte-Carlo (MC) simulations for modeling the intramolecular vibrational motion. These simulations were used to compute thermally-averaged geometrical structures and infrared vibrational intensities for a benchmark set previously studied by gas electron diffraction (GED): CS₂, benzene, chloromethylthiocyanate, pyrazinamide and 9,12-I₂-1,2-closo-C₂B₁₀H₁₀. The MD sampling of NVT ensembles was performed using chains of Nose-Hoover thermostats (NH) as well as the generalized Langevin equation thermostat (GLE). The performance of the theoretical models based on the classical MD and MC simulations was compared with the experimental data and also with the alternative computational techniques: a conventional approach based on the Taylor expansion of potential energy surface, path-integral MD and MD with quantum-thermal bath (QTB) based on the generalized Langevin equation (GLE). A straightforward application of the classical simulations resulted, as expected, in poor accuracy of the calculated observables due to the complete neglect of quantum effects. However, the introduction of a posteriori quantum corrections significantly improved the situation. The application of these corrections for MD simulations of the systems with large-amplitude motions was demonstrated for chloromethylthiocyanate. The comparison of the theoretical vibrational spectra has revealed that the GLE thermostat used in this work is not applicable for this purpose. On the other hand, the NH chains yielded reasonably good results.

Tetranitromethane: A Nightmare of Molecular Flexibility in the Gaseous and Solid States

After numerous attempts over the last seven decades to obtain a structure for the simple, highly symmetric molecule tetranitromethane (C(NO₂ )₄ , TNM) that is consistent with results from diffraction experiments and spectroscopic analysis, the structure has now been determined in the gas phase and the solid state. For the gas phase, a new approach based on a four-dimensional dynamic model for describing the correlated torsional dynamics of the four C-NO₂ units was necessary to describe the experimental gas-phase electron diffraction intensities. A model describing a highly disordered high-temperature crystalline phase was also established, and the structure of an ordered low-temperature phase was determined by X-ray diffraction. TNM is a prime example of molecular flexibility, bringing structural methods to the limits of their applicability.

Planar aromaticity of D N h -symmetrical systems as a perturbed two-dimensional (2D) rigid rotor

Energy levels for D _{N h} -symmetrical cyclic polyenes with planar aromaticity were obtained using two-dimensional (2D) rigid rotor as the zeroth approximation. The addition of nuclei was simulated by the cosine-type potential and treated at the first-order perturbation theory. The result is qualitatively equivalent to that obtained using Hückel's molecular orbital theory. As an addition, the energetic shift between σ and π orbitals is obtained using the model of electron oscillating around the center of a positively charged ring.

The effect of molecular dynamics sampling on the calculated observable gas-phase structures

In this study, we compare the performance of various ab initio molecular dynamics (MD) sampling methods for the calculation of the observable vibrationally-averaged gas-phase structures of benzene, naphthalene and anthracene molecules. Nose-Hoover (NH), canonical and quantum generalized-Langevin-equation (GLE) thermostats as well as the a posteriori quantum correction to the classical trajectories have been tested and compared to the accurate path-integral molecular dynamics (PIMD), static anharmonic vibrational calculations as well as to the experimental gas electron diffraction data. Classical sampling methods neglecting quantum effects (NH and canonical GLE thermostats) dramatically underestimate vibrational amplitudes for the bonded atom pairs, both C-H and C-C, the resulting radial distribution functions exhibit nonphysically narrow peaks. This deficiency is almost completely removed by taking the quantum effects on the nuclei into account. The quantum GLE thermostat and a posteriori correction to the canonical GLE and NH thermostatted trajectories capture most vibrational quantum effects and closely reproduce computationally expensive PIMD and experimental radial distribution functions. These methods are both computationally feasible and accurate and are therefore recommended for calculations of the observable gas-phase structures. A good performance of the quantum GLE thermostat for the gas-phase calculations is encouraging since its parameters have been originally fitted for the condensed-phase calculations. Very accurate molecular structures can be predicted by combining the equilibrium geometry obtained at a high level of electronic structure theory with vibrational amplitudes and corrections calculated using MD driven by a lower level of electronic structure theory.

Gas phase equilibrium structure of histamine

The first gas electron diffraction (GED) experiment for histamine was carried out. The equilibrium structure of histamine in the gas phase was determined on the basis of the data obtained. The refinement was also supported by the rotational constants obtained in previous studies [B. Vogelsanger, et al., J. Am. Chem. Soc., 1991, 113, 7864-7869; P. Godfrey, et al., J. Am. Chem. Soc., 1998, 120, 10724-10732] and quantum chemical calculations. The proposed mechanism of tautomerization by simultaneous intermolecular transfer of hydrogens in a histamine dimer helps to explain the distribution of tautomers in different experiments. The estimations of the conformational interconversion times provided the explanation for the absence of some conformers in the rotational spectroscopy experiments.